3L3C Rna Binding Protein Rna date Dec 16, 2009
title Crystal Structure Of The Bacillus Anthracis Glms Ribozyme Bo Glc6p
authors S.A.Strobel, J.C.Cochrane, S.V.Lipchock, K.D.Smith
compound source
Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: A, B, C, D
Fragment: Rna Binding Domain
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11

Molecule: Rna (5'-R(Ap(A2m)Gpcpgpcpcpapgpapapcp
Chain: E, F, G, H
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Other_details: Synthesized At Dharmacon

Molecule: Glms Ribozyme
Chain: P, Q, R, S
Engineered: Yes

Synthetic: Yes
Other_details: In Vitro Transcribed From A Dna Template
symmetry Space Group: P 1 21 1
R_factor 0.263 R_Free 0.303
length a length b length c angle alpha angle beta angle gamma
47.882 234.947 104.540 90.00 90.55 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand A2M, G6P, GTP, MG enzyme
note 3L3C supersedes 3G95
A, D, C, B

Primary referenceStructural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme., Cochrane JC, Lipchock SV, Smith KD, Strobel SA, Biochemistry. 2009 Apr 21;48(15):3239-46. PMID:19228039
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (322 Kb) [Save to disk]
  • Biological Unit Coordinates (3l3c.pdb1.gz) 80 Kb
  • Biological Unit Coordinates (3l3c.pdb2.gz) 81 Kb
  • Biological Unit Coordinates (3l3c.pdb3.gz) 81 Kb
  • Biological Unit Coordinates (3l3c.pdb4.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 3L3C
  • CSU: Contacts of Structural Units for 3L3C
  • Structure Factors (723 Kb)
  • Retrieve 3L3C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L3C from S2C, [Save to disk]
  • Re-refined 3l3c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3L3C in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3L3C
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3L3C, from MSDmotif at EBI
  • Fold representative 3l3c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l3c_E] [3l3c_H] [3l3c_G] [3l3c_Q] [3l3c_R] [3l3c_A] [3l3c_F] [3l3c_B] [3l3c_D] [3l3c_P] [3l3c_C] [3l3c] [3l3c_S]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM